Contacts of the helix formed by residues 144 - 152 (chain A) in PDB entry 4GL5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 144 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLY 4.1 6.5 + - - +
132A ILE* 3.5 19.3 - - + -
135A ASN* 4.7 0.5 + - - -
140A LEU 2.4 29.2 + - - -
141A TRP* 3.1 1.9 + - - -
143A THR* 1.3 79.4 + - - +
145A ARG* 1.3 67.1 + - - +
146A PRO* 3.3 2.5 - - - -
147A PHE* 3.1 27.1 + - + +
148A PHE* 3.6 5.8 - - + -
282A LEU* 5.3 1.6 - - + -
291A LEU* 5.0 6.3 - - + +
295A ASN* 4.3 16.4 + - - +
299A CYS* 3.5 32.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 3.8 17.2 - - + +
141A TRP* 3.1 38.2 + - + +
142A LYS* 4.5 2.5 - - - +
144A THR* 1.3 77.2 - - - +
146A PRO* 1.4 70.2 - - + +
148A PHE* 2.9 7.3 + - + -
149A MET* 2.8 67.1 + - + +
433A GLY 4.7 2.0 + - - -
434A PRO 3.4 16.4 + - - -
435A ARG* 3.7 7.2 - - - +
436A GLY* 3.0 31.7 + - - +
437A CYS 4.2 1.2 + - - -
438A ALA* 4.2 6.5 - - - +
600A HEM 2.8 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS 3.0 24.7 - - - +
143A THR* 4.2 8.1 - - - +
144A THR 3.3 5.4 - - - +
145A ARG* 1.4 91.2 - - + +
147A PHE* 1.3 61.4 + - + +
149A MET* 3.5 9.1 - - + +
150A LYS* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A THR 3.3 21.8 - - - -
144A THR* 3.1 18.4 + - + +
145A ARG 3.0 0.2 + - - -
146A PRO* 1.3 77.9 - - + +
148A PHE* 1.3 64.8 + - + +
150A LYS* 4.1 4.2 - - - +
151A ALA* 3.4 14.0 + - - +
278A PHE* 3.4 22.4 - - + -
281A GLU* 3.8 38.0 - - + +
282A LEU* 3.6 30.5 - - + -
285A ALA* 3.7 22.0 - - + -
288A ARG* 4.8 7.0 - - - -
290A ASP* 5.3 4.7 - - + -
291A LEU* 3.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 3.5 47.1 - - + -
144A THR 3.6 14.6 - - - -
145A ARG 2.9 6.3 + - - +
147A PHE* 1.3 74.3 - - + +
149A MET* 1.3 66.4 + - + +
151A ALA* 3.3 1.4 + - - -
152A LEU* 3.1 39.6 + - + +
278A PHE* 3.7 16.6 - + - -
299A CYS* 3.6 47.6 - - + -
302A GLU* 4.5 8.7 - - + -
303A MET* 3.4 35.2 - - + -
438A ALA* 4.5 4.3 - - + -
600A HEM 4.3 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ARG* 2.8 67.6 + - + +
146A PRO* 3.2 9.4 + - + +
148A PHE* 1.3 78.6 - - - +
150A LYS* 1.3 59.2 + - - +
152A LEU* 3.8 5.6 + - - +
153A SER* 2.9 23.2 + - - -
437A CYS 5.6 0.7 - - - +
438A ALA* 4.0 21.1 - - + +
441A TYR* 6.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PRO 2.9 16.8 + - - +
147A PHE* 4.1 4.7 - - - +
148A PHE 3.2 0.2 - - - -
149A MET* 1.3 77.6 - - - +
151A ALA* 1.3 62.4 + - - +
152A LEU 3.3 1.0 + - - -
153A SER* 3.3 24.3 + - - +
155A PRO* 5.1 10.6 - - - +
276A MET* 5.3 4.6 + - - +
281A GLU* 3.3 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A PHE 3.4 15.9 + - - +
148A PHE 3.3 3.4 + - - +
150A LYS* 1.3 78.8 - - - +
152A LEU* 1.3 56.3 + - - +
153A SER 3.4 3.9 + - - -
156A GLY* 4.3 15.8 - - - -
202A LEU* 4.5 1.6 - - - +
203A PHE* 3.6 20.8 - - + -
278A PHE* 3.6 36.6 - - + +
281A GLU* 6.5 0.2 - - + -
303A MET* 4.5 1.8 - - + -
442A ILE* 4.7 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A PHE* 3.1 25.6 + - + +
149A MET 4.1 3.4 - - - +
150A LYS 3.2 0.6 - - - -
151A ALA* 1.3 76.1 - - - +
153A SER* 1.3 60.7 + - - +
157A LEU* 4.4 2.6 - - - +
203A PHE* 3.5 29.4 - - + -
303A MET* 3.9 17.7 - - + -
438A ALA* 3.5 46.7 - - + +
439A GLY* 3.9 2.7 - - - +
441A TYR* 4.9 4.5 - - - +
442A ILE* 3.8 47.0 + - + +
600A HEM 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il